Did you download 43 separate bz2 files or 1 bz2 file that extracted to 43 directories?
configure/make is done at the package level. If you download a tarball and unpack it into a working directory, there may be many subdirectories created, but you only need to work from the top level. If you do ./configure -- make -- make install from the top level it will dive into all of the subdirectories and do whatever is necessary.
If you unpacked 43 separate packages into the same top level directory you may have to start over because stuff could get overwritten. I usually create a separate working dir for each package, then unpack into that dir. Once you do that you can kick off as many simultaneous build jobs you can keep track of and that your system can handle.